1 | // =============================================================== // |
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2 | // // |
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3 | // File : ap_tree_nlen.hxx // |
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4 | // Purpose : // |
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5 | // // |
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6 | // Coded by Ralf Westram (coder@reallysoft.de) in Summer 1995 // |
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7 | // Institute of Microbiology (Technical University Munich) // |
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8 | // http://www.arb-home.de/ // |
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9 | // // |
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10 | // =============================================================== // |
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11 | |
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12 | #ifndef AP_TREE_NLEN_HXX |
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13 | #define AP_TREE_NLEN_HXX |
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14 | |
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15 | #ifndef _GLIBCXX_IOSTREAM |
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16 | #include <iostream> |
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17 | #endif |
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18 | #ifndef _GLIBCXX_CLIMITS |
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19 | #include <climits> |
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20 | #endif |
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21 | #ifndef AP_MAIN_HXX |
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22 | #include <ap_main.hxx> |
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23 | #endif |
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24 | |
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25 | class AP_tree_nlen; |
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26 | |
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27 | struct AP_CO_LIST { // liste fuer crossover |
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28 | GBDATA *leaf0; |
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29 | GBDATA *leaf1; |
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30 | int node0; |
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31 | int node1; |
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32 | |
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33 | class AP_tree_nlen *pntr; |
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34 | }; |
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35 | |
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36 | enum AP_KL_FLAG { // flags fuer die Rekursionsart bei Kernighan Lin |
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37 | AP_DYNAMIK = 1, |
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38 | AP_STATIC = 2, |
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39 | AP_BETTER = 4, |
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40 | // Funktionstyp der Schwellwertfunktion |
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41 | AP_QUADRAT_START = 5, |
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42 | AP_QUADRAT_MAX = 6 |
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43 | }; |
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44 | |
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45 | enum AP_BL_MODE { |
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46 | APBL_NONE = 0, |
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47 | AP_BL_NNI_ONLY = 1, // try te find a better tree only |
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48 | AP_BL_BL_ONLY = 2, // try to calculate the branch lengths |
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49 | AP_BL_NNI_BL = 3, // better tree & branch lengths |
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50 | AP_BL_BOOTSTRAP_LIMIT = 4, // calculate upper bootstrap limits |
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51 | AP_BL_BOOTSTRAP_ESTIMATE = 12 // calculate estimate of bootstrap (includes AP_BL_BOOTSTRAP_LIMIT) |
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52 | }; |
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53 | |
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54 | class AP_tree_edge; |
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55 | |
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56 | class AP_tree_nlen : public AP_tree { // derived from a Noncopyable |
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57 | // tree that is independent of branch lengths and root |
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58 | |
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59 | AP_TREE_SIDE kernighan; // Flag zum markieren |
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60 | int distance; // distance to tree border (0=leaf, INT_MAX=UNKNOWN) |
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61 | |
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62 | // definitions for AP_tree_edge: |
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63 | |
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64 | AP_tree_edge *edge[3]; // the edges to the father and the sons |
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65 | int index[3]; // index to node[] in AP_tree_edge |
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66 | |
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67 | AP_FLOAT mutation_rate; |
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68 | |
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69 | |
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70 | |
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71 | void createListRekUp(AP_CO_LIST *list, int *cn); |
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72 | void createListRekSide(AP_CO_LIST *list, int *cn); |
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73 | |
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74 | public: |
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75 | explicit AP_tree_nlen(AP_tree_root *troot) |
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76 | : AP_tree(troot), |
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77 | kernighan(AP_NONE), |
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78 | distance(INT_MAX), |
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79 | mutation_rate(0) |
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80 | { |
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81 | edge[0] = edge[1] = edge[2] = NULL; |
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82 | index[0] = index[1] = index[2] = 0; |
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83 | } |
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84 | ~AP_tree_nlen() OVERRIDE {} |
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85 | |
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86 | DEFINE_TREE_ACCESSORS(AP_tree_root, AP_tree_nlen); |
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87 | |
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88 | void unhash_sequence(); |
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89 | AP_FLOAT costs(char *mutPerSite = NULL); // cost of a tree (number of changes ..) |
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90 | |
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91 | bool push(AP_STACK_MODE, unsigned long); // push state of costs |
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92 | void pop(unsigned long); // pop old tree costs |
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93 | bool clear(unsigned long stack_update, unsigned long user_push_counter); |
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94 | |
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95 | virtual AP_UPDATE_FLAGS check_update() OVERRIDE; // disable load !!!! |
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96 | |
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97 | void copy(AP_tree_nlen *tree); |
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98 | int Distance(); |
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99 | |
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100 | // tree reconstruction methods: |
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101 | void insert(AP_tree_nlen *new_brother); |
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102 | void initial_insert(AP_tree_nlen *new_brother, AP_tree_root *troot); |
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103 | |
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104 | void remove() OVERRIDE; |
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105 | void swap_sons() OVERRIDE; |
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106 | void swap_assymetric(AP_TREE_SIDE mode) OVERRIDE; |
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107 | void moveNextTo(AP_tree_nlen *new_brother, AP_FLOAT rel_pos); // if unsure, use cantMoveNextTo to test if possible |
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108 | void set_root() OVERRIDE; |
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109 | |
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110 | // overload virtual methods from AP_tree: |
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111 | void insert(AP_tree *new_brother) OVERRIDE { insert(DOWNCAST(AP_tree_nlen*, new_brother)); } |
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112 | void initial_insert(AP_tree *new_brother, AP_tree_root *troot) OVERRIDE { initial_insert(DOWNCAST(AP_tree_nlen*, new_brother), troot); } |
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113 | void moveNextTo(AP_tree *node, AP_FLOAT rel_pos) OVERRIDE { moveNextTo(DOWNCAST(AP_tree_nlen*, node), rel_pos); } |
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114 | |
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115 | // tree optimization methods: |
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116 | void parsimony_rek(char *mutPerSite = NULL); |
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117 | |
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118 | AP_FLOAT nn_interchange_rek(int deep, // -1 means: do whole subtree |
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119 | AP_BL_MODE mode, |
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120 | bool skip_hidden); |
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121 | |
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122 | AP_FLOAT nn_interchange(AP_FLOAT parsimony, AP_BL_MODE mode); |
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123 | |
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124 | void kernighan_rek(int rek_deep, |
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125 | int *rek_breite, |
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126 | int rek_breite_anz, |
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127 | const int rek_deep_max, |
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128 | double (*function)(double, double *, int), |
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129 | double *param_liste, |
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130 | int param_anz, |
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131 | AP_FLOAT pars_best, |
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132 | AP_FLOAT pars_start, |
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133 | AP_FLOAT pars_prev, |
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134 | AP_KL_FLAG searchflag, |
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135 | bool *abort_flag); |
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136 | |
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137 | // for crossover creates a list of 3 times the nodes with all |
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138 | // ancestors in it |
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139 | AP_CO_LIST * createList(int *size); |
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140 | |
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141 | class AP_tree_stack stack; // tree stack |
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142 | |
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143 | // misc stuff: |
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144 | |
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145 | void setBranchlen(double leftLen, double rightLen) { leftlen = leftLen; rightlen = rightLen; } |
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146 | |
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147 | const char* fullname() const; |
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148 | const char* sortByName(); |
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149 | |
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150 | // AP_tree_edge access functions: |
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151 | |
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152 | int indexOf(const AP_tree_edge *e) const { int i; for (i=0; i<3; i++) if (edge[i]==e) return i; return -1; } |
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153 | |
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154 | AP_tree_edge* edgeTo(const AP_tree_nlen *brother) const; |
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155 | AP_tree_edge* nextEdge(const AP_tree_edge *afterThatEdge=NULL) const; |
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156 | int unusedEdgeIndex() const; // [0..2], -1 if none |
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157 | |
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158 | // more complex edge functions: |
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159 | |
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160 | void linkAllEdges(AP_tree_edge *edge1, AP_tree_edge *edge2, AP_tree_edge *edge3); |
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161 | void unlinkAllEdges(AP_tree_edge **edgePtr1, AP_tree_edge **edgePtr2, AP_tree_edge **edgePtr3); |
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162 | |
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163 | char *getSequenceCopy(); |
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164 | |
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165 | #if defined(PROVIDE_TREE_STRUCTURE_TESTS) |
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166 | void assert_edges_valid() const; |
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167 | void assert_valid() const; |
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168 | #endif // PROVIDE_TREE_STRUCTURE_TESTS |
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169 | |
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170 | |
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171 | friend class AP_tree_edge; |
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172 | friend std::ostream& operator<<(std::ostream&, const AP_tree_nlen&); |
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173 | }; |
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174 | |
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175 | struct AP_TreeNlenNodeFactory : public RootedTreeNodeFactory { |
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176 | RootedTree *makeNode(TreeRoot *root) const OVERRIDE { |
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177 | return new AP_tree_nlen(DOWNCAST(AP_tree_root*, root)); |
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178 | } |
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179 | }; |
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180 | |
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181 | // --------------------- |
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182 | // AP_tree_edge |
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183 | |
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184 | class MutationsPerSite; |
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185 | |
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186 | class AP_tree_edge : virtual Noncopyable { |
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187 | // the following members are stored/restored by |
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188 | // AP_tree_nlen::push/pop: |
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189 | |
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190 | AP_tree_nlen *node[2]; // the two nodes of this edge |
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191 | int index[2]; // index to edge[] in AP_tree_nlen |
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192 | AP_tree_edge_data data; // data stored in edge (defined in AP_buffer.hxx) |
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193 | |
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194 | // and these arent pushed: |
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195 | |
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196 | AP_tree_edge *next; // temporary next pointer used by some methods |
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197 | int used; // test-counter |
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198 | long age; // age of the edge |
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199 | |
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200 | static long timeStamp; // static counter for edge-age |
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201 | // recursive methods: |
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202 | // |
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203 | // deep: determines how deep we go into the tree |
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204 | // -1 means we go through the whole tree |
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205 | // 0 means we only act on the actual edge |
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206 | |
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207 | AP_tree_edge *buildChain(int deep, |
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208 | bool skip_hidden = false, |
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209 | int distance = 0, |
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210 | const AP_tree_nlen *skip = NULL, |
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211 | AP_tree_edge *comesFrom = NULL); |
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212 | |
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213 | long sizeofChain(); |
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214 | void calcDistance(); |
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215 | void tailDistance(AP_tree_nlen*); |
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216 | |
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217 | int distanceOK() const { int diff = node[0]->distance-node[1]->distance; return diff>=-1 && diff<=1; } |
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218 | |
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219 | // my friends: |
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220 | |
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221 | friend class AP_tree_nlen; |
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222 | friend std::ostream& operator<<(std::ostream&, const AP_tree_edge&); |
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223 | #if defined(UNIT_TESTS) // UT_DIFF |
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224 | friend void TEST_tree_modifications(); |
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225 | #endif |
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226 | |
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227 | protected: |
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228 | |
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229 | ~AP_tree_edge(); |
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230 | |
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231 | // relink & unlink (they are also used by constructor & destructor) |
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232 | |
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233 | void relink(AP_tree_nlen *node1, AP_tree_nlen *node2); |
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234 | AP_tree_edge *unlink(); |
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235 | |
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236 | public: |
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237 | |
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238 | AP_tree_edge(AP_tree_nlen *node1, AP_tree_nlen *node2); |
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239 | |
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240 | static void initialize(AP_tree_nlen *root); |
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241 | static void destroy(AP_tree_nlen *root); |
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242 | |
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243 | // access methods: |
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244 | |
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245 | int isConnectedTo(const AP_tree_nlen *n) const { return node[0]==n || node[1]==n; } |
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246 | int indexOf(const AP_tree_nlen *n) const { ap_assert(isConnectedTo(n)); return node[1] == n; } |
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247 | AP_tree_nlen* otherNode(const AP_tree_nlen *n) const { return node[1-indexOf(n)]; } |
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248 | AP_tree_nlen* sonNode() const { return node[0]->get_father() == node[1] ? node[0] : node[1]; } |
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249 | AP_tree_edge* Next() const { return next; } |
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250 | long Age() const { return age; } |
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251 | |
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252 | // encapsulated AP_tree_nlen methods: |
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253 | |
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254 | void set_root() { return sonNode()->set_root(); } |
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255 | |
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256 | // tree optimization: |
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257 | |
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258 | AP_FLOAT nni_rek(int deep, bool skip_hidden, AP_BL_MODE mode, AP_tree_nlen *skipNode); |
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259 | |
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260 | AP_FLOAT calc_branchlengths() { return nni_rek(-1, false, AP_BL_BL_ONLY, NULL); } |
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261 | |
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262 | AP_FLOAT nni_mutPerSite(AP_FLOAT pars_one, AP_BL_MODE mode, MutationsPerSite *mps); |
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263 | AP_FLOAT nni(AP_FLOAT pars_one, AP_BL_MODE mode) { return nni_mutPerSite(pars_one, mode, NULL); } |
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264 | |
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265 | // test methods: |
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266 | |
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267 | void mixTree(int cnt); |
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268 | int test() const; |
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269 | int dumpChain() const; |
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270 | void testChain(int deep); |
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271 | |
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272 | int Distance() const { ap_assert(distanceOK()); return (node[0]->distance+node[1]->distance) >> 1; } |
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273 | int distanceToBorder(int maxsearch=INT_MAX, AP_tree_nlen *skipNode=NULL) const; // obsolete |
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274 | |
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275 | static int dumpNNI; // should NNI dump its values? |
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276 | static int distInsertBorder; // distance from insert pos to tree border |
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277 | static int basesChanged; // no of bases which were changed |
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278 | // in fathers sequence because of insertion |
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279 | |
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280 | void countSpecies(int deep=-1, const AP_tree_nlen* skip=NULL); |
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281 | |
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282 | static int speciesInTree; // no of species (leafs) in tree (updated by countSpecies) |
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283 | static int nodesInTree; // no of nodes in tree - including leafs, but w/o rootnode (updated by countSpecies) |
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284 | |
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285 | static int edgesInTree() { return nodesInTree-1; } // (updated by countSpecies) |
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286 | }; |
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287 | |
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288 | std::ostream& operator<<(std::ostream&, const AP_tree_edge&); |
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289 | |
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290 | |
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291 | inline AP_tree_nlen *rootNode() { |
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292 | return ap_main->get_root_node(); |
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293 | } |
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294 | |
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295 | inline AP_tree_edge *rootEdge() { |
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296 | return rootNode()->get_leftson()->edgeTo(rootNode()->get_rightson()); |
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297 | } |
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298 | |
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299 | #else |
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300 | #error ap_tree_nlen.hxx included twice |
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301 | #endif // AP_TREE_NLEN_HXX |
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